Abstract: Cryo-Electron Microscopy (cryo-EM) is an increasingly popular experimental technique for estimating the 3D structure of macromolecular complexes such as proteins based on 2D images. These images are notoriously noisy, and the pose of the structure in each image is unknown $\textit{a priori}$. Ab-initio 3D reconstruction from 2D images entails estimating the pose in addition to the structure. In this work, we propose a new approach to this problem. We first adopt a multi-head architecture as a pose encoder to infer multiple plausible poses per-image in an amortized fashion. This approach mitigates the high uncertainty in pose estimation by encouraging exploration of pose space early in reconstruction. Once uncertainty is reduced, we refine poses in an auto-decoding fashion. In particular, we initialize with the most likely pose and iteratively update it for individual images using stochastic gradient descent (SGD). Through evaluation on synthetic datasets, we demonstrate that our method is able to handle multi-modal pose distributions during the amortized inference stage, while the later, more flexible stage of direct pose optimization yields faster and more accurate convergence of poses compared to baselines. Finally, on experimental data, we show that our approach is faster than state-of-the-art cryoAI and achieves higher-resolution reconstruction.